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Related Concept Videos

Multi-pass Transmembrane Proteins and β-barrels01:09

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In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Published on: July 16, 2017

Structure-based statistical analysis of transmembrane helices.

Carlos Baeza-Delgado1, Marc A Marti-Renom, Ismael Mingarro

  • 1Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Spain.

European Biophysics Journal : EBJ
|May 17, 2012
PubMed
Summary
This summary is machine-generated.

Integral membrane proteins have specific amino acid patterns in transmembrane helices. Hydrophobic amino acids dominate TM segments, while charged residues prefer interfaces, supporting the "positive-inside rule".

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Membrane Protein Research

Background:

  • High-resolution structures of membrane proteins are now available for detailed analysis.
  • Understanding amino acid composition in transmembrane (TM) segments is crucial for membrane protein function.

Purpose of the Study:

  • To analyze the prevalent locations and distributions of amino acids within TM helices of integral membrane proteins.
  • To compare amino acid patterns in TM helices with those in water-soluble helical proteins.

Main Methods:

  • Large-scale analysis using a dataset of 170 integral membrane protein structures (MPtopo database).
  • Comparison with 930 water-soluble helical protein structures (Protein Data Bank).

Main Results:

  • Hydrophobic amino acids (Leu, Val, Ile, Phe) and Gly are prevalent in TM helices.
  • Polar amino acids are less frequent in TM helices.
  • Hydrophobic/slightly polar residues are in the membrane core; aromatic, Pro, and hydrophilic residues are at interfaces.
  • Charged amino acids are outside the hydrophobic core; acidic residues are at both interfaces, basic residues cluster at the cytoplasmic interface.

Conclusions:

  • Structural data strongly support the biased distribution of positively charged amino acids, known as the "positive-inside rule".
  • Amino acid distribution in TM helices is non-random and dictated by the membrane environment.